Package picard.vcf
Class CollectVariantCallingMetrics.VariantCallingDetailMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
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- picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
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- Enclosing class:
- CollectVariantCallingMetrics
public static class CollectVariantCallingMetrics.VariantCallingDetailMetrics extends CollectVariantCallingMetrics.VariantCallingSummaryMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
Fields Modifier and Type Field Description doubleHET_HOMVAR_RATIO(count of hets)/(count of homozygous non-ref) for this sampledoublePCT_GQ0_VARIANTSThe percentage of variants in a particular sample that have a GQ score of 0.StringSAMPLE_ALIASThe name of the sample being assayedlongTOTAL_GQ0_VARIANTSThe total number of variants in a particular sample that have a GQ score of 0.longTOTAL_HET_DEPTHtotal number of reads (from AD field) for passing bi-allelic SNP hets for this sample-
Fields inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
DBSNP_INS_DEL_RATIO, DBSNP_TITV, FILTERED_INDELS, FILTERED_SNPS, NOVEL_INDELS, NOVEL_INS_DEL_RATIO, NOVEL_SNPS, NOVEL_TITV, NUM_IN_DB_SNP, NUM_IN_DB_SNP_COMPLEX_INDELS, NUM_IN_DB_SNP_INDELS, NUM_IN_DB_SNP_MULTIALLELIC, NUM_SINGLETONS, PCT_DBSNP, PCT_DBSNP_INDELS, SNP_REFERENCE_BIAS, TOTAL_COMPLEX_INDELS, TOTAL_INDELS, TOTAL_MULTIALLELIC_SNPS, TOTAL_SNPS
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Constructor Summary
Constructors Constructor Description VariantCallingDetailMetrics()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description voidcalculateDerivedFields()Placeholder method that will calculate the derived fields from the other ones.voidcalculateFromDerivedFields()static StringgetFileExtension()-
Methods inherited from class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
calculateFromDerivedFields, foldInto
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Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample being assayed
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HET_HOMVAR_RATIO
public double HET_HOMVAR_RATIO
(count of hets)/(count of homozygous non-ref) for this sample
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PCT_GQ0_VARIANTS
public double PCT_GQ0_VARIANTS
The percentage of variants in a particular sample that have a GQ score of 0.
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TOTAL_GQ0_VARIANTS
public long TOTAL_GQ0_VARIANTS
The total number of variants in a particular sample that have a GQ score of 0.
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TOTAL_HET_DEPTH
public long TOTAL_HET_DEPTH
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
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Method Detail
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getFileExtension
public static String getFileExtension()
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calculateDerivedFields
public void calculateDerivedFields()
Description copied from class:MergeableMetricBasePlaceholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated withNoMergingKeepsValue.- Overrides:
calculateDerivedFieldsin classCollectVariantCallingMetrics.VariantCallingSummaryMetrics
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calculateFromDerivedFields
public void calculateFromDerivedFields()
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